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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.33

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        MultiQC is developed by Seqera.

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        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2026-02-13, 21:21 -03 based on data in: /dados01/jorge/TATIANA/run2/01_fastqc
        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        General Statistics

        Showing 152/152 rows and 3/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        Sample_IDSW36_D09_S54_R1_001
        84.7%
        55.0%
        150bp
        150bp
        27%
        22.6M
        Sample_IDSW36_D09_S54_R2_001
        38.7%
        54.0%
        150bp
        150bp
        18%
        22.6M
        Sample_IDSW37_E09_S55_R1_001
        86.5%
        56.0%
        150bp
        150bp
        27%
        21.8M
        Sample_IDSW37_E09_S55_R2_001
        43.1%
        55.0%
        150bp
        150bp
        18%
        21.8M
        Sample_IDSW38_A01_S56_R1_001
        83.3%
        56.0%
        150bp
        150bp
        27%
        12.0M
        Sample_IDSW38_A01_S56_R2_001
        34.8%
        55.0%
        150bp
        150bp
        18%
        12.0M
        Sample_IDSW38_F09_S57_R1_001
        88.3%
        55.0%
        150bp
        150bp
        27%
        17.7M
        Sample_IDSW38_F09_S57_R2_001
        47.7%
        54.0%
        150bp
        150bp
        18%
        17.7M
        Sample_IDSW39_C01_S58_R1_001
        81.6%
        56.0%
        150bp
        150bp
        27%
        20.3M
        Sample_IDSW39_C01_S58_R2_001
        37.6%
        54.0%
        150bp
        150bp
        18%
        20.3M
        Sample_IDSW40_B01_S59_R1_001
        81.4%
        56.0%
        150bp
        150bp
        27%
        15.6M
        Sample_IDSW40_B01_S59_R2_001
        39.7%
        54.0%
        150bp
        150bp
        18%
        15.6M
        Sample_IDSW45_D01_S60_R1_001
        63.1%
        55.0%
        150bp
        150bp
        27%
        8.3M
        Sample_IDSW45_D01_S60_R2_001
        23.3%
        54.0%
        150bp
        150bp
        18%
        8.3M
        Sample_IDSW46_E01_S61_R1_001
        87.3%
        56.0%
        150bp
        150bp
        27%
        16.4M
        Sample_IDSW46_E01_S61_R2_001
        43.1%
        55.0%
        150bp
        150bp
        18%
        16.4M
        Sample_IDSW47_F01_S62_R1_001
        77.8%
        54.0%
        150bp
        150bp
        27%
        10.5M
        Sample_IDSW47_F01_S62_R2_001
        33.5%
        53.0%
        150bp
        150bp
        18%
        10.5M
        Sample_IDSW48_G01_S63_R1_001
        72.7%
        54.0%
        150bp
        150bp
        27%
        13.5M
        Sample_IDSW48_G01_S63_R2_001
        23.8%
        52.0%
        150bp
        150bp
        18%
        13.5M
        Sample_IDSW50_H01_S64_R1_001
        80.7%
        55.0%
        150bp
        150bp
        27%
        11.5M
        Sample_IDSW50_H01_S64_R2_001
        35.2%
        54.0%
        150bp
        150bp
        18%
        11.5M
        Sample_IDSW51_A02_S65_R1_001
        71.7%
        57.0%
        150bp
        150bp
        27%
        12.9M
        Sample_IDSW51_A02_S65_R2_001
        20.2%
        56.0%
        150bp
        150bp
        18%
        12.9M
        Sample_IDSW53_G02_S66_R1_001
        84.3%
        56.0%
        150bp
        150bp
        27%
        22.9M
        Sample_IDSW53_G02_S66_R2_001
        35.8%
        54.0%
        150bp
        150bp
        18%
        22.9M
        Sample_IDSW55_B02_S67_R1_001
        86.9%
        56.0%
        150bp
        150bp
        27%
        18.6M
        Sample_IDSW55_B02_S67_R2_001
        35.6%
        55.0%
        150bp
        150bp
        18%
        18.6M
        Sample_IDSW56_C02_S68_R1_001
        83.2%
        54.0%
        150bp
        150bp
        27%
        17.2M
        Sample_IDSW56_C02_S68_R2_001
        33.5%
        52.0%
        150bp
        150bp
        18%
        17.2M
        Sample_IDSW57_D02_S69_R1_001
        88.8%
        56.0%
        150bp
        150bp
        27%
        20.2M
        Sample_IDSW57_D02_S69_R2_001
        39.9%
        55.0%
        150bp
        150bp
        18%
        20.2M
        Sample_IDSW58_E02_S70_R1_001
        88.4%
        55.0%
        150bp
        150bp
        27%
        23.7M
        Sample_IDSW58_E02_S70_R2_001
        41.2%
        53.0%
        150bp
        150bp
        18%
        23.7M
        Sample_IDSW59_F02_S71_R1_001
        81.4%
        53.0%
        150bp
        150bp
        27%
        8.9M
        Sample_IDSW59_F02_S71_R2_001
        35.3%
        51.0%
        150bp
        150bp
        18%
        8.9M
        Sample_IDSW61_A03_S72_R1_001
        86.7%
        57.0%
        150bp
        150bp
        27%
        17.7M
        Sample_IDSW61_A03_S72_R2_001
        35.8%
        55.0%
        150bp
        150bp
        18%
        17.7M
        Sample_IDSW62_B03_S73_R1_001
        86.7%
        56.0%
        150bp
        150bp
        27%
        23.5M
        Sample_IDSW62_B03_S73_R2_001
        40.4%
        54.0%
        150bp
        150bp
        18%
        23.5M
        Sample_IDSW67_C03_S74_R1_001
        50.7%
        55.0%
        150bp
        150bp
        27%
        6.0M
        Sample_IDSW67_C03_S74_R2_001
        15.9%
        52.0%
        150bp
        150bp
        18%
        6.0M
        Sample_IDSW70_D03_S75_R1_001
        48.5%
        58.0%
        150bp
        150bp
        18%
        8.3M
        Sample_IDSW70_D03_S75_R2_001
        13.4%
        55.0%
        150bp
        150bp
        18%
        8.3M
        Sample_IDSW70_G09_S76_R1_001
        43.4%
        58.0%
        150bp
        150bp
        18%
        11.2M
        Sample_IDSW70_G09_S76_R2_001
        9.4%
        56.0%
        150bp
        150bp
        18%
        11.2M
        Sample_IDSW71_H09_S77_R1_001
        31.6%
        58.0%
        150bp
        150bp
        18%
        12.4M
        Sample_IDSW71_H09_S77_R2_001
        7.3%
        58.0%
        150bp
        150bp
        18%
        12.4M
        Sample_IDSW72_A10_S78_R1_001
        33.1%
        58.0%
        150bp
        150bp
        18%
        6.1M
        Sample_IDSW72_A10_S78_R2_001
        9.3%
        57.0%
        150bp
        150bp
        18%
        6.1M
        Sample_IDSW74_B10_S79_R1_001
        29.3%
        61.0%
        150bp
        150bp
        18%
        6.5M
        Sample_IDSW74_B10_S79_R2_001
        7.9%
        59.0%
        150bp
        150bp
        18%
        6.5M
        Sample_IDSW74_E03_S80_R1_001
        39.4%
        60.0%
        150bp
        150bp
        18%
        7.7M
        Sample_IDSW74_E03_S80_R2_001
        9.6%
        58.0%
        150bp
        150bp
        18%
        7.7M
        Sample_IDSW81_B04_S81_R1_001
        50.8%
        59.0%
        150bp
        150bp
        27%
        4.6M
        Sample_IDSW81_B04_S81_R2_001
        14.1%
        57.0%
        150bp
        150bp
        18%
        4.6M
        Sample_IDSW82_C04_S82_R1_001
        42.1%
        56.0%
        150bp
        150bp
        27%
        5.5M
        Sample_IDSW82_C04_S82_R2_001
        13.0%
        54.0%
        150bp
        150bp
        18%
        5.5M
        Sample_IDSW84_D04_S83_R1_001
        41.0%
        58.0%
        150bp
        150bp
        18%
        13.5M
        Sample_IDSW84_D04_S83_R2_001
        8.0%
        56.0%
        150bp
        150bp
        18%
        13.5M
        Sample_IDSW85_E04_S84_R1_001
        48.7%
        52.0%
        150bp
        150bp
        18%
        7.8M
        Sample_IDSW85_E04_S84_R2_001
        18.2%
        51.0%
        150bp
        150bp
        18%
        7.8M
        Sample_IDSW114_F03_S4_R1_001
        44.5%
        54.0%
        150bp
        150bp
        18%
        5.2M
        Sample_IDSW114_F03_S4_R2_001
        15.7%
        52.0%
        150bp
        150bp
        18%
        5.2M
        Sample_IDSW115_G03_S5_R1_001
        47.8%
        55.0%
        150bp
        150bp
        27%
        7.4M
        Sample_IDSW115_G03_S5_R2_001
        14.3%
        53.0%
        150bp
        150bp
        18%
        7.4M
        Sample_IDSW116_H03_S6_R1_001
        54.4%
        52.0%
        150bp
        150bp
        27%
        4.6M
        Sample_IDSW116_H03_S6_R2_001
        24.8%
        50.0%
        150bp
        150bp
        18%
        4.6M
        Sample_IDSW118_A04_S7_R1_001
        51.1%
        52.0%
        150bp
        150bp
        27%
        4.3M
        Sample_IDSW118_A04_S7_R2_001
        19.7%
        51.0%
        150bp
        150bp
        18%
        4.3M
        Sample_IDSW126_G08_S8_R1_001
        36.9%
        56.0%
        150bp
        150bp
        27%
        5.5M
        Sample_IDSW126_G08_S8_R2_001
        11.1%
        53.0%
        150bp
        150bp
        18%
        5.5M
        Sample_IDSW127_H08_S9_R1_001
        51.1%
        53.0%
        150bp
        150bp
        27%
        4.3M
        Sample_IDSW127_H08_S9_R2_001
        21.0%
        52.0%
        150bp
        150bp
        18%
        4.3M
        Sample_IDSW129_A09_S10_R1_001
        48.3%
        54.0%
        150bp
        150bp
        18%
        6.4M
        Sample_IDSW129_A09_S10_R2_001
        20.3%
        53.0%
        150bp
        150bp
        18%
        6.4M
        Sample_IDSW130_B09_S11_R1_001
        36.5%
        57.0%
        150bp
        150bp
        18%
        10.2M
        Sample_IDSW130_B09_S11_R2_001
        10.4%
        56.0%
        150bp
        150bp
        18%
        10.2M
        Sample_IDSW140_H04_S13_R1_001
        43.8%
        57.0%
        150bp
        150bp
        18%
        8.4M
        Sample_IDSW140_H04_S13_R2_001
        14.1%
        56.0%
        150bp
        150bp
        18%
        8.4M
        Sample_IDSW145_C05_S17_R1_001
        35.2%
        58.0%
        150bp
        150bp
        18%
        7.3M
        Sample_IDSW145_C05_S17_R2_001
        10.3%
        56.0%
        150bp
        150bp
        18%
        7.3M
        Sample_IDSW145_D11_S18_R1_001
        35.3%
        59.0%
        150bp
        150bp
        18%
        10.2M
        Sample_IDSW145_D11_S18_R2_001
        7.7%
        57.0%
        150bp
        150bp
        18%
        10.2M
        Sample_IDSW146_D05_S19_R1_001
        27.2%
        59.0%
        150bp
        150bp
        18%
        6.9M
        Sample_IDSW146_D05_S19_R2_001
        6.7%
        57.0%
        150bp
        150bp
        18%
        6.9M
        Sample_IDSW147_E10_S20_R1_001
        41.2%
        57.0%
        150bp
        150bp
        18%
        13.0M
        Sample_IDSW147_E10_S20_R2_001
        12.1%
        56.0%
        150bp
        150bp
        18%
        13.0M
        Sample_IDSW150_F05_S22_R1_001
        31.5%
        58.0%
        150bp
        150bp
        18%
        4.7M
        Sample_IDSW150_F05_S22_R2_001
        8.8%
        57.0%
        150bp
        150bp
        18%
        4.7M
        Sample_IDSW156_G05_S23_R1_001
        84.9%
        56.0%
        150bp
        150bp
        27%
        13.1M
        Sample_IDSW156_G05_S23_R2_001
        36.3%
        55.0%
        150bp
        150bp
        18%
        13.1M
        Sample_IDSW157_H05_S24_R1_001
        35.9%
        55.0%
        150bp
        150bp
        27%
        3.2M
        Sample_IDSW157_H05_S24_R2_001
        15.6%
        54.0%
        150bp
        150bp
        18%
        3.2M
        Sample_IDSW158_B06_S25_R1_001
        63.9%
        57.0%
        150bp
        150bp
        27%
        10.1M
        Sample_IDSW158_B06_S25_R2_001
        21.0%
        56.0%
        150bp
        150bp
        18%
        10.1M
        Sample_IDSW159_C09_S26_R1_001
        81.5%
        57.0%
        150bp
        150bp
        27%
        19.8M
        Sample_IDSW159_C09_S26_R2_001
        30.0%
        55.0%
        150bp
        150bp
        18%
        19.8M
        Sample_IDSW161_C06_S27_R1_001
        56.8%
        52.0%
        150bp
        150bp
        27%
        7.0M
        Sample_IDSW161_C06_S27_R2_001
        24.1%
        50.0%
        150bp
        150bp
        18%
        7.0M
        Sample_IDSW162_D06_S28_R1_001
        43.7%
        56.0%
        150bp
        150bp
        18%
        7.1M
        Sample_IDSW162_D06_S28_R2_001
        16.3%
        54.0%
        150bp
        150bp
        18%
        7.1M
        Sample_IDSW163_E06_S29_R1_001
        73.2%
        56.0%
        150bp
        150bp
        27%
        13.9M
        Sample_IDSW163_E06_S29_R2_001
        24.2%
        55.0%
        150bp
        150bp
        18%
        13.9M
        Sample_IDSW164_F06_S30_R1_001
        31.0%
        59.0%
        150bp
        150bp
        18%
        8.2M
        Sample_IDSW164_F06_S30_R2_001
        7.8%
        57.0%
        150bp
        150bp
        18%
        8.2M
        Sample_IDSW165_G06_S31_R1_001
        55.9%
        53.0%
        150bp
        150bp
        27%
        7.7M
        Sample_IDSW165_G06_S31_R2_001
        21.3%
        52.0%
        150bp
        150bp
        18%
        7.7M
        Sample_IDSW166_H06_S32_R1_001
        68.5%
        54.0%
        150bp
        150bp
        27%
        9.1M
        Sample_IDSW166_H06_S32_R2_001
        30.5%
        53.0%
        150bp
        150bp
        18%
        9.1M
        Sample_IDSW183_A07_S33_R1_001
        41.4%
        59.0%
        150bp
        150bp
        18%
        6.8M
        Sample_IDSW183_A07_S33_R2_001
        11.4%
        58.0%
        150bp
        150bp
        18%
        6.8M
        Sample_IDSW184_F10_S34_R1_001
        26.2%
        61.0%
        150bp
        150bp
        18%
        12.1M
        Sample_IDSW184_F10_S34_R2_001
        4.3%
        60.0%
        150bp
        150bp
        18%
        12.1M
        Sample_IDSW186_G10_S35_R1_001
        38.0%
        60.0%
        150bp
        150bp
        18%
        11.9M
        Sample_IDSW186_G10_S35_R2_001
        7.7%
        58.0%
        150bp
        150bp
        18%
        11.9M
        Sample_IDSW187_F04_S36_R1_001
        25.7%
        60.0%
        150bp
        150bp
        18%
        5.7M
        Sample_IDSW187_F04_S36_R2_001
        5.6%
        59.0%
        150bp
        150bp
        18%
        5.7M
        Sample_IDSW190_H10_S37_R1_001
        27.8%
        60.0%
        150bp
        150bp
        18%
        10.9M
        Sample_IDSW190_H10_S37_R2_001
        5.8%
        59.0%
        150bp
        150bp
        18%
        10.9M
        Sample_IDSW191_B07_S38_R1_001
        39.6%
        60.0%
        150bp
        150bp
        18%
        8.0M
        Sample_IDSW191_B07_S38_R2_001
        10.7%
        58.0%
        150bp
        150bp
        18%
        8.0M
        Sample_IDSW192_F07_S39_R1_001
        28.7%
        60.0%
        150bp
        150bp
        18%
        7.1M
        Sample_IDSW192_F07_S39_R2_001
        7.0%
        58.0%
        150bp
        150bp
        18%
        7.1M
        Sample_IDSW193_C07_S40_R1_001
        39.2%
        57.0%
        150bp
        150bp
        18%
        3.2M
        Sample_IDSW193_C07_S40_R2_001
        10.9%
        55.0%
        150bp
        150bp
        18%
        3.2M
        Sample_IDSW194_D07_S41_R1_001
        34.8%
        60.0%
        150bp
        150bp
        18%
        8.6M
        Sample_IDSW194_D07_S41_R2_001
        7.8%
        58.0%
        150bp
        150bp
        18%
        8.6M
        Sample_IDSW196_E07_S42_R1_001
        33.7%
        57.0%
        150bp
        150bp
        18%
        6.0M
        Sample_IDSW196_E07_S42_R2_001
        11.1%
        56.0%
        150bp
        150bp
        18%
        6.0M
        Sample_IDSW198_G07_S43_R1_001
        44.9%
        59.0%
        150bp
        150bp
        18%
        8.6M
        Sample_IDSW198_G07_S43_R2_001
        11.2%
        57.0%
        150bp
        150bp
        18%
        8.6M
        Sample_IDSW199_A11_S44_R1_001
        25.8%
        59.0%
        150bp
        150bp
        18%
        5.3M
        Sample_IDSW199_A11_S44_R2_001
        7.1%
        57.0%
        150bp
        150bp
        18%
        5.3M
        Sample_IDSW199_H07_S45_R1_001
        41.4%
        55.0%
        150bp
        150bp
        18%
        5.1M
        Sample_IDSW199_H07_S45_R2_001
        16.2%
        54.0%
        150bp
        150bp
        27%
        5.1M
        Sample_IDSW200_B11_S46_R1_001
        40.0%
        59.0%
        150bp
        150bp
        18%
        11.6M
        Sample_IDSW200_B11_S46_R2_001
        9.8%
        57.0%
        150bp
        150bp
        18%
        11.6M
        Sample_IDSW201_C11_S47_R1_001
        20.7%
        63.0%
        150bp
        150bp
        18%
        7.3M
        Sample_IDSW201_C11_S47_R2_001
        4.2%
        60.0%
        150bp
        150bp
        18%
        7.3M
        Sample_IDSW220_A08_S48_R1_001
        17.4%
        60.0%
        150bp
        150bp
        18%
        7.2M
        Sample_IDSW220_A08_S48_R2_001
        2.9%
        58.0%
        150bp
        150bp
        18%
        7.2M
        Sample_IDSW224_B08_S49_R1_001
        29.4%
        56.0%
        150bp
        150bp
        18%
        3.2M
        Sample_IDSW224_B08_S49_R2_001
        9.3%
        54.0%
        150bp
        150bp
        18%
        3.2M
        Sample_IDSW231_C08_S50_R1_001
        35.8%
        60.0%
        150bp
        150bp
        18%
        7.1M
        Sample_IDSW231_C08_S50_R2_001
        6.9%
        57.0%
        150bp
        150bp
        18%
        7.1M
        Sample_IDSW232_F08_S51_R1_001
        36.5%
        59.0%
        150bp
        150bp
        18%
        5.7M
        Sample_IDSW232_F08_S51_R2_001
        8.8%
        56.0%
        150bp
        150bp
        18%
        5.7M
        Sample_IDSW234_E08_S52_R1_001
        31.7%
        59.0%
        150bp
        150bp
        18%
        4.3M
        Sample_IDSW234_E08_S52_R2_001
        7.5%
        56.0%
        150bp
        150bp
        18%
        4.3M
        Sample_IDSW235_D08_S53_R1_001
        40.7%
        61.0%
        150bp
        150bp
        18%
        8.3M
        Sample_IDSW235_D08_S53_R2_001
        8.4%
        58.0%
        150bp
        150bp
        18%
        8.3M
        Expand table

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms
        152

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores
        152

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        $ Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content
        102
        45
        5

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content
        152

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution
        152

        All samples have sequences of a single length (150bp)

        Sequence Duplication Levels
        66
        54
        32

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        AACTACGGACCCTTTATCATAACCTCTGCTCGTTGCATACCCTGATCCAC
        17
        185818
        0.0120%
        CGTACGGACCCTTTATCATAACCTCTGCTCGTTGCATACCCTGATCCACT
        13
        122684
        0.0079%
        GTACTACGGACCCTTTATCATAACCTCTGCTCGTTGCATACCCTGATCCA
        13
        115629
        0.0074%
        AACTACGGCAGAAGGGAAGCGCGGATTCAAAGCTCAGGCCACCGCCAAAA
        1
        58239
        0.0037%
        TGCGGACCCTTTATCATAACCTCTGCTCGTTGCATACCCTGATCCACTAC
        7
        48367
        0.0031%
        ATCTTGCAGGTACTTCTGGATTCAGAGGCACAAGAAAAGGAACACCCTAT
        7
        47715
        0.0031%
        AACTACGGGTGCCCAGGTATCATATACGCCTCCAAAATAAAGAGCCTTGA
        7
        42810
        0.0028%
        ACTCTATGCACATCTGACGCTGCCGACGAGTAATAATGTGTAGATCTCGG
        3
        34453
        0.0022%
        ACTCTATGCACATCTGACGCTGCCGACGACTTCAATCGTGTAGATCTCGG
        3
        33335
        0.0021%
        TCTCTTATACACATCTCCGAGCCCACGAGACCATGGTCAATCTCGTATGC
        4
        30301
        0.0019%
        TCTCTTATACACATCTCCGAGCCCACGAGACGGCAGCCAATCTCGTATGC
        4
        27429
        0.0018%
        TGCGGAGATATGGATAAAATATCTAGGCACAGCGGCATTTTGATACCACC
        4
        24779
        0.0016%
        TGCAGGTACTTCTGGATTCAGAGGCACAAGAAAAGGAACACCCTATGCTG
        3
        20774
        0.0013%
        AACTACGGGGCCATTATTCCTACTTCCGCAGCTATAGGTTTACATTTTTA
        3
        19921
        0.0013%
        TCTCTTATACACATCTCCGAGCCCACGAGACTTGGCTGAATCTCGTATGC
        2
        18156
        0.0012%
        AACTACGGAGATATGGATAAAATATCTAGGCACAGCGGCATTTTGATACC
        2
        14103
        0.0009%
        ACTCTATGCACATCTGACGCTGCCGACGATCATTACGGTGTAGATCTCGG
        2
        12408
        0.0008%
        CGTGCAGGTACTTCTGGATTCAGAGGCACAAGAAAAGGAACACCCTATGC
        2
        11677
        0.0008%
        TCGGACCCTTTATCATAACCTCTGCTCGTTGCATACCCTGATCCACTACT
        2
        11615
        0.0007%
        GTACTACGGGTGCCCAGGTATCATATACGCCTCCAAAATAAAGAGCCTTG
        2
        9608
        0.0006%
        Expand table

        Adapter Content
        152

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1